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"Yes," Juan Tomas agreed. "That you must do. But I wonder if you will find it any different in the capital. Here, you have friends and me, your brother. There, you will have no one."
Through this comment we can see that Juan Carlo worries about Kino. He knows how tough possession of the pearl has been in a place where he (kino) is well known and considered a friend. Going away to the capital will isolate him completely from the people who care about him. There will be no friends and no safety.